The State Department, concerned about possible new congressional moves to cut military aid to El Salvador, denied yesterday that recent legislation by the rightist-dominated Constituent Assembly there will block a U.S.-supported land reform program.

Essentially, the department contended that clarifications issued in El Salvador about the legislation's intent contained reassurances that the land reform will continue.

But, the department said, it will take some time to determine the actual effects of the new law, and it added: "We will continue to watch the situation very closely to ensure that it implementation does in fact continue."

That was the gist of several highly technical and confusing statements issued by department spokesmen in response to news reports from El Salvador that the rightists, who form the majority in the recently elected assembly, intend to halt further large-scale redistribution of land in that civil-war wracked country.

The issue is one of potentially acute sensitivity for the Reagan administration's policy of providing continued military and economic aid to Salvadoran authorities fighting leftist guerrilla efforts to win control of El Salvador.

The administration has seized on the land reform program as a symbol of its argument that change can be brought about in El Salvador through peaceful processes. Prior to the Constituent Assembly elections at the end of March, the administration stressed repeatedly that decisions about U.S. aid would depend in part on continuation of successful land reform.

Similarly, Congress specified that, as one condition for continuing aid, President Reagan must certify that Salvadoran authorities are making "continued progress in implementing essential economic and political reforms, including the land reform program . . . . " The president, who made such a certification early this year, must do so again next month.

Last week, when the Salvadoran assembly passed the legislation, it provoked an angry outcry from key congressional leaders, including Sen. Charles H. Percy (R-Ill.), chairman of the Foreign Relations Committee. He and other committee members warned that if land reform is halted, they will fight to cut off all assistance to El Salvador.

Confronted by these rumblings in Congress, the administration pleaded for more time to allow for clarification. Its renewal of that plea yesterday underscored the difficulties it faces in trying to prod El Salvador's reluctant rightists to continue economic and social reform programs.

At issue is legislation dealing with medium-sized land holdings. The original intent was to exempt temporarily from expropriation lands in this category used for growing cotton and sugar cane. That is to give owners an incentive to continue planting these crops, which are badly needed to generate exports.

In passing the law, however, the majority rightists attached several provisions that would exempt lands used for cereals, corn and livestock. The effect, as the State Department conceded yesterday, "confirmed the indefinite deferral" of that phase of the land reform dealing with medium-sized holdings.

However, the department, pointing to statements by Salvadoran leaders, said it understands that peasant tenant farmers, working the land in this category, would not lose their rights to acquire the small plots they have been farming.

Despite these assurances, U.S. officials privately believe the new law went too far, and efforts are understood to be under way to induce the assembly to limit its provisions to cotton and sugar cane land, or failing that, to encourage Salvadoran President Alvaro Magana to veto the legislation.